PDB-6qgm: VirX1 apo structure

ID or keywords:

Entry

Database: PDB / ID: 6qgm

Title

VirX1 apo structure

Components

VirX1

Keywords

HYDROLASE / Iodinase / viral halogenase / FDH

Function / homology

Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / FAD/NAD(P)-binding domain superfamily / Uncharacterized protein

Function and homology information

Biological species

Cyanophage Syn10 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Gkotsi, D.S. / Ludewig, H. / Sharma, S.V. / Unsworth, W.P. / Taylor, R.J.K. / McLachlan, M.M.W. / Shanahan, S. / Naismith, J.H. / Goss, R.J.M.

Funding support

United Kingdom, 1items

Citation

Journal: Nat.Chem. / Year: 2019
Title: A marine viral halogenase that iodinates diverse substrates.
Authors: Gkotsi, D.S. / Ludewig, H. / Sharma, S.V. / Connolly, J.A. / Dhaliwal, J. / Wang, Y. / Unsworth, W.P. / Taylor, R.J.K. / McLachlan, M.M.W. / Shanahan, S. / Naismith, J.H. / Goss, R.J.M.

History

Deposition	Jan 11, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 30, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2019	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6qgm.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb6qgm.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	6qgm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qg/6qgm ftp://data.pdbj.org/pub/pdb/validation_reports/qg/6qgm	HTTPS FTP

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Related structure data

Related structure data	2weuS S: Starting model for refinement
Similar structure data	2gv9-2 6grh-d 6gos-d 7btx-d 6gri-d 5dlq-2 2gn6-1 3lrl-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

a: VirX1

b: VirX1

c: VirX1

d: VirX1

e: VirX1

f: VirX1

368 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

a: VirX1

b: VirX1

c: VirX1

defined by author&software
Evidence: gel filtration
184 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

d: VirX1

e: VirX1

f: VirX1

defined by author&software
184 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.133, 172.979, 110.425
Angle α, β, γ (deg.)	90.000, 112.890, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	VAL	GLY	GLY	a	A	5 - 531	2 - 528
2	1	VAL	VAL	GLY	GLY	b	B	5 - 531	2 - 528
1	2	VAL	VAL	ILE	ILE	a	A	5 - 529	2 - 526
2	2	VAL	VAL	ILE	ILE	c	C	5 - 529	2 - 526
1	3	VAL	VAL	SER	SER	a	A	5 - 532	2 - 529
2	3	VAL	VAL	SER	SER	d	D	5 - 532	2 - 529
1	4	LYS	LYS	TYR	TYR	a	A	6 - 530	3 - 527
2	4	LYS	LYS	TYR	TYR	e	E	6 - 530	3 - 527
1	5	LYS	LYS	GLY	GLY	a	A	6 - 531	3 - 528
2	5	LYS	LYS	GLY	GLY	f	F	6 - 531	3 - 528
1	6	VAL	VAL	ILE	ILE	b	B	5 - 529	2 - 526
2	6	VAL	VAL	ILE	ILE	c	C	5 - 529	2 - 526
1	7	VAL	VAL	GLY	GLY	b	B	5 - 531	2 - 528
2	7	VAL	VAL	GLY	GLY	d	D	5 - 531	2 - 528
1	8	LYS	LYS	TYR	TYR	b	B	6 - 530	3 - 527
2	8	LYS	LYS	TYR	TYR	e	E	6 - 530	3 - 527
1	9	LYS	LYS	ALA	ALA	b	B	6 - 533	3 - 530
2	9	LYS	LYS	ALA	ALA	f	F	6 - 533	3 - 530
1	10	VAL	VAL	ILE	ILE	c	C	5 - 529	2 - 526
2	10	VAL	VAL	ILE	ILE	d	D	5 - 529	2 - 526
1	11	LYS	LYS	ILE	ILE	c	C	6 - 529	3 - 526
2	11	LYS	LYS	ILE	ILE	e	E	6 - 529	3 - 526
1	12	LYS	LYS	ILE	ILE	c	C	6 - 529	3 - 526
2	12	LYS	LYS	ILE	ILE	f	F	6 - 529	3 - 526
1	13	LYS	LYS	TYR	TYR	d	D	6 - 530	3 - 527
2	13	LYS	LYS	TYR	TYR	e	E	6 - 530	3 - 527
1	14	LYS	LYS	GLY	GLY	d	D	6 - 531	3 - 528
2	14	LYS	LYS	GLY	GLY	f	F	6 - 531	3 - 528
1	15	LYS	LYS	TYR	TYR	e	E	6 - 530	3 - 527
2	15	LYS	LYS	TYR	TYR	f	F	6 - 530	3 - 527

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	VirX1 Mass: 61306.555 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanophage Syn10 (virus) / Gene: CPUG_00131 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M4SKV1
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10.43 mg/mL 0.1 M Tris HCl pH 8.5 0.2 M magnesium chloride hexahydrate 30% w/v polyethylene glycol 4,000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.9763 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 2.75→172.979 Å / Num. obs: 89551 / % possible obs: 99.1 % / Redundancy: 3.4 % / CC_1/2: 0.994 / R_merge(I) obs: 0.1 / R_pim(I) all: 0.064 / R_rim(I) all: 0.119 / Net I/σ(I): 9.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2.753-2.8	3.5	0.589	4467	0.697	0.367	0.696	99.5
7.472-172.979	3.3	0.041	4470	0.996	0.027	0.049	96.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0232	refinement
Aimless		data scaling
PDB_EXTRACT	3.24	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2WEU

2weu

Resolution: 2.75→87.94 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.879 / SU B: 40.72 / SU ML: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.399
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2589	4356	4.9 %	RANDOM
R_work	0.2158	-	-	-
obs	0.2179	85159	99.04 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å

Displacement parameters

B_iso max: 124.99 Å² / B_iso mean: 60.943 Å² / B_iso min: 22.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.74 Å²	0 Å²	2.88 Å²
2-	-	-3.46 Å²	0 Å²
3-	-	-	1.31 Å²

Refinement step

Cycle: final / Resolution: 2.75→87.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25640	0	0	48	25688
B_iso mean	-	-	-	44.79	-
Num. residues	-	-	-	-	3145

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	26368
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	22998
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.642	35719
X-RAY DIFFRACTION	r_angle_other_deg	1.217	1.576	53529
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.547	5	3133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.056	23.127	1519
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.818	15	4353
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.925	15	126
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	3305
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	29777
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5893

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	a	17866	0.07
1	2	b	17866	0.07
2	1	a	17708	0.07
2	2	c	17708	0.07
3	1	a	17873	0.08
3	2	d	17873	0.08
4	1	a	17848	0.07
4	2	e	17848	0.07
5	1	a	17804	0.07
5	2	f	17804	0.07
6	1	b	17600	0.08
6	2	c	17600	0.08
7	1	b	17877	0.07
7	2	d	17877	0.07
8	1	b	17850	0.07
8	2	e	17850	0.07
9	1	b	17943	0.07
9	2	f	17943	0.07
10	1	c	17663	0.07
10	2	d	17663	0.07
11	1	c	17659	0.08
11	2	e	17659	0.08
12	1	c	17630	0.08
12	2	f	17630	0.08
13	1	d	17884	0.07
13	2	e	17884	0.07
14	1	d	17946	0.07
14	2	f	17946	0.07
15	1	e	17814	0.08
15	2	f	17814	0.08

LS refinement shell

Resolution: 2.753→2.824 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.357	309	-
R_work	0.333	6338	-
all	-	6647	-
obs	-	-	99.91 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.348	-0.0201	1.3238	2.0137	0.8635	5.1467	-0.0284	-0.2804	-0.2298	-0.1212	0.0808	-0.1164	-0.0409	-0.0154	-0.0524	0.0954	-0.0068	0.0434	0.1668	0.1063	0.1765	35.314	-62.301	-28.289
2	0.5384	-0.0866	0.0145	1.6865	0.0608	1.178	-0.0177	-0.1078	-0.1124	0.3759	-0.0207	0.0992	0.0097	-0.0666	0.0384	0.1495	0.0114	0.0068	0.457	0.0987	0.0883	44.03	-45.208	-3.211
3	0.9096	0.3391	0.3593	0.7138	0.128	0.6328	-0.0303	-0.005	-0.24	-0.0463	0.0053	-0.1801	0.093	0.2034	0.025	0.0815	0.05	0.0578	0.3116	0.0743	0.1146	48.656	-54.791	-29.741
4	0.509	0.2337	0.2432	0.5376	0.106	0.2737	0.0001	-0.1587	-0.0613	0.1807	0.0153	-0.0388	-0.0663	-0.0778	-0.0153	0.1634	0.0403	0.0198	0.4053	0.0745	0.0367	40.497	-38.661	-14.053
5	1.9645	2.4045	-0.7451	5.1721	-1.2143	1.2671	0.1555	0.0881	0.1361	0.2044	0.0164	0.0702	-0.1944	-0.1083	-0.1719	0.1007	0.1158	0.0645	0.3752	-0.0027	0.16	-8.336	-18.591	-32.967
6	2.3003	-1.3073	0.3576	2.133	-0.8224	1.2923	-0.0552	-0.2689	-0.1595	0.2612	0.1726	0.3069	-0.0925	-0.095	-0.1174	0.081	-0.0239	0.0613	0.2973	0.0164	0.0566	-1.047	-47.616	-21.667
7	0.3115	-0.0774	-0.1463	1.3708	-0.0014	0.4385	0.0743	0.0833	0.0524	-0.1762	0.0066	0.1739	-0.0851	-0.0223	-0.0809	0.1124	0.0027	0.0191	0.3462	0.0197	0.0659	1.145	-29.475	-40.862
8	4.7359	-1.1095	0.7068	1.6922	-0.4374	1.0707	-0.0705	-0.3275	0.056	0.3175	0.0737	-0.0163	0.0407	-0.0257	-0.0032	0.1132	-0.0444	0.0296	0.2422	-0.0608	0.0308	5.012	-51.691	-17.985
9	0.8598	-0.3887	0.1497	1.1731	-0.1251	0.3517	-0.0357	-0.2372	0.1797	0.1067	-0.0084	-0.1525	-0.0539	0.0349	0.0441	0.293	-0.0088	0.0509	0.4036	-0.0496	0.0589	33.513	-3.118	-8.299
10	1.2498	-0.7165	0.6389	1.7592	-0.1116	0.5616	0.0151	0.0057	0.3583	-0.0985	-0.1072	-0.2217	-0.0822	0.0463	0.0921	0.2465	-0.0082	0.1161	0.3258	-0.0064	0.1722	35.257	5.55	-21.48
11	0.0003	0.023	0.0059	6.8243	2.2413	0.7539	-0.0141	-0.0048	0.0055	0.261	0.1039	-0.0379	0.0901	0.0542	-0.0898	0.3068	0.0234	-0.0252	0.3094	-0.0188	0.2596	29.119	-0.924	-19.808
12	0.6514	-0.3475	0.1955	0.5062	-0.05	0.1366	-0.0151	-0.136	0.023	0.2071	-0.028	0.0969	0.0337	-0.0909	0.0431	0.2877	0.0054	0.1056	0.4326	-0.0435	0.0955	19.49	-10.307	-14.842
13	2.9641	1.3588	1.1983	1.3145	0.546	5.3717	-0.1542	-0.1442	-0.1049	-0.1346	-0.1056	-0.0154	0.0179	0.2373	0.2598	0.2579	0.1313	0.1065	0.3559	0.0007	0.1631	24.964	-42.704	38.986
14	1.9273	-0.1921	0.0635	0.3916	-0.1359	1.1489	0.0143	0.1124	-0.0995	-0.2415	-0.0379	-0.0603	0.1172	0.0611	0.0236	0.5115	0.0257	0.0428	0.3103	-0.0656	0.0324	2.863	-44.165	14.481
15	0.8154	0.3593	0.2546	0.5788	0.2125	0.4326	-0.0261	0.0314	-0.2272	-0.1098	0.0169	-0.1258	0.2033	0.116	0.0093	0.3835	0.0489	0.0688	0.339	0.0166	0.0874	10.345	-47.021	37.187
16	1.3812	-0.2236	0.1378	0.7523	0.1875	1.6073	0.0993	0.2414	0.0056	-0.2243	-0.0882	-0.0051	-0.1101	0.0482	-0.0111	0.4279	-0.0353	0.058	0.3192	-0.0812	0.0597	-2.055	-37.702	12.811
17	4.1649	-0.2585	-1.826	2.3996	0.8695	2.0594	0.0108	0.1273	0.053	0.3146	-0.0935	-0.2129	0.2323	0.1576	0.0827	0.2566	-0.0534	-0.0354	0.1831	0.0492	0.0547	3.976	14.633	43.73
18	1.1698	-0.474	-0.1448	1.2931	0.2853	0.2294	-0.0812	-0.0084	0.177	0.3086	0.0593	-0.1664	0.0696	0.1315	0.0219	0.3325	-0.0479	-0.0575	0.3758	0.0319	0.0603	17.174	3.662	45.951
19	2.4613	0.0022	-0.7969	0.1688	0.4106	1.2756	0.0127	0.1441	0.0573	0.0192	0.0725	-0.043	0.0647	0.1548	-0.0853	0.2711	-0.0366	-0.0084	0.2996	-0.0344	0.1789	0.315	4.107	41.167
20	0.9026	-0.3776	-0.0895	1.2427	-0.0549	0.3234	-0.1332	0.1869	-0.1325	-0.0526	0.0541	-0.0642	0.0854	0.0764	0.079	0.3111	-0.0027	0.0233	0.4575	0.0098	0.0472	21.731	-13.27	35.429
21	0.3702	0.3892	-0.0874	1.4868	-0.6775	0.5551	0.0238	0.0477	-0.0075	-0.1706	0.0466	0.2196	0.2472	-0.062	-0.0705	0.274	-0.0187	-0.022	0.332	-0.0471	0.065	-28.522	-18.428	19.293
22	0.6388	0.6454	0.1138	2.551	0.1046	2.1319	0.1543	-0.1959	0.4558	0.3188	-0.3213	0.6105	0.0664	-0.2596	0.167	0.1805	-0.1324	0.1209	0.4525	-0.1545	0.3407	-37.327	-3.69	28.6
23	0.1816	-0.3527	-0.0357	1.9753	-0.2429	0.2376	0.1254	0.0084	-0.0084	0.0211	-0.1712	0.1295	0.054	-0.0594	0.0457	0.3394	-0.0757	0.0535	0.3879	-0.0643	0.0535	-22.271	-17.707	32.067
24	1.1448	1.1392	1.0418	1.7105	0.3552	1.8638	-0.0688	0.2061	-0.0576	-0.1297	0.0134	-0.1264	-0.0878	0.2545	0.0554	0.1785	0.0996	0.0075	0.3585	-0.036	0.0218	-11.902	3.644	15.764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	a	5 - 63
2	X-RAY DIFFRACTION	2	a	64 - 165
3	X-RAY DIFFRACTION	3	a	166 - 344
4	X-RAY DIFFRACTION	4	a	345 - 532
5	X-RAY DIFFRACTION	5	b	5 - 69
6	X-RAY DIFFRACTION	6	b	70 - 165
7	X-RAY DIFFRACTION	7	b	166 - 450
8	X-RAY DIFFRACTION	8	b	451 - 533
9	X-RAY DIFFRACTION	9	c	5 - 213
10	X-RAY DIFFRACTION	10	c	214 - 352
11	X-RAY DIFFRACTION	11	c	353 - 359
12	X-RAY DIFFRACTION	12	c	360 - 532
13	X-RAY DIFFRACTION	13	d	6 - 64
14	X-RAY DIFFRACTION	14	d	65 - 146
15	X-RAY DIFFRACTION	15	d	147 - 437
16	X-RAY DIFFRACTION	16	d	438 - 550
17	X-RAY DIFFRACTION	17	e	6 - 63
18	X-RAY DIFFRACTION	18	e	64 - 351
19	X-RAY DIFFRACTION	19	e	352 - 390
20	X-RAY DIFFRACTION	20	e	391 - 531
21	X-RAY DIFFRACTION	21	f	6 - 243
22	X-RAY DIFFRACTION	22	f	244 - 322
23	X-RAY DIFFRACTION	23	f	323 - 449
24	X-RAY DIFFRACTION	24	f	450 - 533

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